Contacts of the helix formed by residues 49 - 61 (chain B) in PDB entry 4I6U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASN 4.6 1.1 - - - +
48B LEU* 1.3 79.4 - - - +
50B ILE* 1.3 69.1 + - - +
51B LYS* 4.0 0.2 - - - +
52B SER* 3.2 24.9 + - - -
53B LEU* 2.9 22.9 + - - +
47C ASN* 3.0 32.4 + - - +
48C LEU* 3.3 14.1 - - - +
49C THR* 4.0 19.5 - - + -
50C ILE* 5.2 0.4 - - - -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 1.3 71.4 - - - +
51B LYS* 1.3 62.7 + - - +
53B LEU* 3.2 13.7 + - + +
54B GLU* 3.0 20.4 + - - +
68B PHE* 6.1 2.0 - - + -
3C SER* 5.2 0.2 - - - +
5C LEU* 3.5 29.8 - - + +
6C LEU* 3.6 29.2 - - + +
9C VAL* 4.5 14.8 - - + -
47C ASN* 3.5 0.6 + - - +
48C LEU* 3.0 36.8 + - + +
49C THR 5.4 0.2 - - - +
50C ILE* 3.7 26.9 - - + -
53C LEU* 4.4 17.5 - - + -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 3.2 0.6 - - - +
50B ILE* 1.3 75.9 - - - +
52B SER* 1.3 60.4 + - - +
54B GLU* 3.3 19.6 + - - +
55B LEU* 3.2 29.3 + - + +
3C SER* 4.7 12.3 - - - +
6C LEU* 4.1 21.6 - - + +
47C ASN* 3.1 32.1 + - - +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 4.2 5.9 - - - +
37B PHE* 3.8 34.4 - - - -
48B LEU* 4.3 5.4 - - - -
49B THR* 3.2 24.0 + - - -
51B LYS* 1.3 74.9 - - - +
53B LEU* 1.3 60.8 + - - +
55B LEU* 3.2 13.5 + - - +
56B ILE* 2.9 31.9 + - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.0 16.6 - - + -
13B ILE* 4.1 14.1 - - + -
48B LEU* 3.9 10.2 - - + +
49B THR 2.9 13.2 + - - +
50B ILE* 3.4 24.9 - - + +
52B SER* 1.3 76.0 - - - +
54B GLU* 1.3 57.8 + - - +
56B ILE* 3.1 6.5 + - + +
57B MET* 2.8 42.0 + - + +
67B PHE* 3.8 33.4 - - + -
68B PHE* 4.2 29.2 - - + -
5C LEU* 4.7 3.4 - - + -
50C ILE* 4.6 9.9 - - + -
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE 3.0 11.2 + - - +
51B LYS* 3.4 15.3 - - - +
52B SER 3.2 0.2 - - - -
53B LEU* 1.3 76.1 - - - +
55B LEU* 1.3 62.0 + - + +
57B MET* 3.2 22.8 + - + +
58B LYS* 3.1 37.9 + - + +
3C SER* 2.5 36.6 + - - -
4C PHE* 3.6 13.2 + - - +
5C LEU* 3.2 28.5 + - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER* 3.6 28.0 - - - +
32B ASN* 5.8 1.8 - - + +
33B LEU* 4.2 24.2 - - + -
51B LYS* 3.2 21.3 + - + +
52B SER* 3.2 11.6 + - - +
54B GLU* 1.3 76.2 - - + +
56B ILE* 1.3 58.2 + - - +
58B LYS* 3.3 28.3 + - + +
59B GLY 2.9 23.2 + - - -
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.0 29.4 - - + -
27B LEU* 4.1 8.7 - - + +
31B SER* 3.8 6.5 - - - +
33B LEU* 3.7 20.6 - - + -
37B PHE* 4.9 1.1 - - + -
38B ILE* 4.2 10.5 - - + -
41B ILE* 3.7 30.5 - - + -
48B LEU* 3.9 13.7 - - + -
52B SER 2.9 19.7 + - - +
53B LEU* 3.1 10.1 + - + +
55B LEU* 1.3 74.3 - - - +
57B MET* 1.3 60.9 + - + +
59B GLY* 3.2 2.3 + - - -
60B LEU* 2.8 46.4 + - + +
67B PHE* 5.8 0.2 - - + -
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Residues in contact with MET 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 2.8 24.6 + - + +
54B GLU* 3.2 37.7 - - + +
55B LEU 3.4 0.2 - - - -
56B ILE* 1.3 73.0 - - - +
58B LYS* 1.3 58.0 + - + +
60B LEU* 3.3 3.6 + - - -
61B GLU 2.9 22.7 + - - -
62B VAL* 3.0 33.3 + - + +
64B ASP* 3.8 29.6 - - + +
67B PHE* 4.2 33.0 - - + -
68B PHE* 4.9 3.1 - - - -
5C LEU* 3.6 27.8 - - + -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 5.1 1.5 + - - +
54B GLU* 3.1 28.8 + - + +
55B LEU* 3.5 28.4 - - - +
57B MET* 1.3 76.7 - - + +
59B GLY* 1.3 61.7 + - - +
61B GLU* 3.1 21.5 + - - +
62B VAL 5.1 1.1 - - - -
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B MET* 3.6 10.9 - - - +
27B LEU* 4.0 5.8 - - - -
30B LYS* 3.5 43.0 + - - +
31B SER* 3.7 15.3 - - - -
55B LEU 2.9 11.7 + - - -
56B ILE 3.2 4.0 + - - -
58B LYS* 1.3 78.8 - - - +
60B LEU* 1.3 57.7 + - - +
61B GLU* 3.6 1.0 + - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.1 13.7 - - - +
16B ILE* 3.8 24.0 - - + +
17B ARG* 3.6 37.2 - - + +
20B LYS* 2.9 30.0 + - + +
22B MET* 4.5 10.7 - - - +
27B LEU* 3.9 19.7 - - + -
56B ILE* 2.8 38.3 + - + +
57B MET* 3.7 5.2 - - - +
59B GLY* 1.3 70.6 - - - +
61B GLU* 1.3 61.6 + - - +
62B VAL* 3.4 17.7 + - + -
67B PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 3.1 16.8 + - - +
30B LYS* 2.9 26.6 + - - +
57B MET 2.9 6.0 + - - -
58B LYS* 3.1 17.1 + - - +
59B GLY 4.3 3.6 - - - +
60B LEU* 1.3 78.7 - - - +
62B VAL* 1.4 58.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il